Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CCMK1 WITH RESIDUES 103-113 DELETED
 
Authors :  M. S. Kimber, B. Samborska
Date :  08 Jul 11  (Deposition) - 11 Jul 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Bacterial Microcompartment Fold, Shell Forming, Structural, Pore Forming, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Samborska, M. S. Kimber
A Ccmk2 Double Layer Is The Dominant Architectural Feature Of The Beta-Carboxysomal Shell Facet
Structure 2012
PubMed: search

(-) Compounds

Molecule 1 - CARBON DIOXIDE CONCENTRATING MECHANISM PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-102
    Gene: CCMK1, TLL0946
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Strain: BP-1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG D:92 , GLU D:95BINDING SITE FOR RESIDUE CL D 111

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SSS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SSS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SSS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SSS)

(-) Exons   (0, 0)

(no "Exon" information available for 3SSS)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:105
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:105
                                    11        21        31        41        51        61        71        81        91       101     
         Q8DKB3_THEEB     2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESVSG 106
               SCOP domains d3sssa_ A: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeehhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3sss A   2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELEHH 106
                                    11        21        31        41        51        61        71        81        91       101     


Chain B from PDB  Type:PROTEIN  Length:102
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:102
                                    12        22        32        42        52        62        72        82        92       102  
         Q8DKB3_THEEB     3 IAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESV 104
               SCOP domains d3sssb_ B: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh......eeeeeee...hhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3sss B   3 IAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELE 104
                                    12        22        32        42        52        62        72        82        92       102  


Chain C from PDB  Type:PROTEIN  Length:103
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
         Q8DKB3_THEEB     2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESV 104
               SCOP domains d3sssc_ C: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeeee.....hhhhh.....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3sss C   2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELE 104
                                    11        21        31        41        51        61        71        81        91       101   


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
         Q8DKB3_THEEB     2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESVS 105
               SCOP domains d3sssd_ D: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3sss D   2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELEH 105
                                    11        21        31        41        51        61        71        81        91       101    


Chain E from PDB  Type:PROTEIN  Length:106
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:106
                                    12        22        32        42        52        62        72        82        92       102      
         Q8DKB3_THEEB     3 IAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESVSGIR 108
               SCOP domains d3ssse_ E: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhh.....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3sss E   3 IAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELEHHHH 108
                                    12        22        32        42        52        62        72        82        92       102      


Chain F from PDB  Type:PROTEIN  Length:103
 aligned with Q8DKB3_THEEB | Q8DKB3 from UniProtKB/TrEMBL  Length:113

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
         Q8DKB3_THEEB     2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRESV 104
               SCOP domains d3sssf_ F: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3sss F   2 AIAVGMIETLGFPAVVEAADAMVKAARVTLVGYEKIGSGRVTVIVRGDVSEVQASVAAGVENVKRVNGGQVLSTHIIARPHENLEYVLPIRYTEAVEQFRELE 104
                                    11        21        31        41        51        61        71        81        91       101
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SSS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SSS)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3SSS)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sss)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3sss
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8DKB3_THEEB | Q8DKB3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8DKB3_THEEB | Q8DKB3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3SSS)

(-) Related Entries Specified in the PDB File

3ssq 3ssr